RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

Co-crystallization experiments of proteins with nucleic acids do not guarantee that both components are present in the crystal. We have previously developed DIBER to predict crystal content when protein and DNA are present in the crystallization mix. Here, we present RIBER, which should be used when protein and RNA are in the crystallization drop. The combined RIBER/DIBER suite builds on machine learning techniques to make reliable, quantitative predictions of crystal content for non-expert users and high-throughput crystallography.     

Responses of the toxic cyanobacterium Microcystis aeruginosa to iron and humic substances.

Iron is an essential element to marine biota. Different types of dissolved organic matter (DOM), such as humic substances have impacts on the marine coastal waters iron chemistry. The aim of the study was to examine how the presence of humic substances (both aquatic and sedimentary) may affect iron bioavailability to the bloom-forming cyanobacterium Microcystis aeruginosa Kutzing incubated on standard and modified mineral BG-11 media. The final iron concentrations in the growth media ranged from 0.1 to 100microM. The results demonstrate that both the growth rate and the concentration of chlorophyll a in cultures of M. aeruginosa are limited by insufficient (<10microM) Fe concentrations. The addition of aquatic humic substances in the presence of iron in concentrations <0.1microM increased the optical density 25-fold, and the production of chlorophyll a 15-fold as compared with the cultures exposed to iron only at the same concentration. Sedimentary humic acids in the presence of iron at a concentration of 10microM reduced the growth and production of chlorophyll a by 50% as compared to the cultures exposed to iron only at the same concentration. Possible mechanisms of humic substances - metal ion - alga interactions are discussed. It is suggested that aquatic humic substances could be of great importance in the formation of cyanobacteria blooms.     

Affinity of dinucleotide cap analogues for human decapping scavenger (hDcpS)

Eukaryotic cells utilize scavenger decapping enzymes to degrade cap structure following 3'-5' mRNA decay. Human DcpS recently has been described as a highly specific hydrolase (a member of the HIT family) that catalyses the cleavage of m(7)GpppG and short capped oligoribonucleotides. We have demonstrated here that cap-1 (m(7)GpppGm) is a preferred substrate among several investigated dinucleotide cap analogues m(7)Gp(n)N (n = 3-5, N is a purine or pyrimidine base) and m(7)GMP is always one of the reaction product. Cap analogues containing pyrimidine base instead of guanine or diphosphate chain are resistant to hydrolysis catalyzed by human scavenger. Contrary to the other enzymes of HIT family, hDcpS activity is not stimulated by Mg(2+).     

Disappearance of differences in antibiotic resistance of Staphylococcus aureus strains isolated in hospitals and in general practice

There is general opinion that Staphylococcus aureus strains isolated in hospitals are more frequently resistant to antibiotics than community strains, however, the increasing resemblance between hospital and community strains has been recently reported. The aim of the study was to compare the antibiotic resistance and phage-type pattern of S. aureus strains isolated from patients treated either in hospitals or in general practice in northern part of Poland. The study was conducted on 771 S. aureus strains isolated from different specimens. Phage typing was performed according to the method of Blair and Williams. The drug susceptibility was determined by the disc-diffusion method. There were no significant differences in antibiotic resistance or phage-type pattern when hospital and community methicillin-sensitive S. aureus (MSSA) strains were compared. The most MSSA were resistant to penicillin (84.6% and 82.1% respectively) and doxycycline (49.3% and 50.4% respectively) whereas they were rarely resistant to other antibiotics. The predominance of phage group II was found in both hospitals (28.0%) and general practice (29.9%). Phage group III, usually associated with hospitals, occurred in small percentage (12.9% and 9.4% respectively) while to this group predominantly (76.6%) multiresistant methicillin resistant S. aureus (MRSA) isolated in hospitals belonged. These results suggest, that there is only slight difference in antibiotic resistance between hospital and community S. aureus strains. Antibiotic resistance pattern mainly results from frequency of appearance of MRSA, mostly occurring in hospitals.     

Helicobacter pylori infection and antioxidants can modulate the genotoxic effects of heterocyclic amines in gastric mucosa cells

Helicobacter pylori (H. pylori) infection plays an important role in gastric carcinogenesis. This bacterium may induce cancer transformation and change the susceptibility of gastric mucosa cells to various exogenous dietary irritants. The aim of the study was to evaluate the influence of H. pylori infection on the reaction of the stomach cells to a genotoxic effect of heterocyclic amines (HCAs). These well-known mutagens are formed during cooking of protein-rich foods, primarily meat. Taking into account that persons consuming a mixed-western diet are exposed to these compound nearly an entire lifetime and more than half of human population is infected with H. pylori, it is important to assess the combined effect of H. pylori infection and HCAs in the context of DNA damage in gastric mucosa cells, which is a prerequisite to cancer transformation. We employed 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), 2-amino-3,8-dimethyl-imidazo[4,5-f]quinoxaline (MeIQx) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) because these substances are present in a great amount in cooked and fried meat. Using alkaline comet assay, we showed that the extent of the DNA damage induced by HCAs was significantly higher in H. pylori infected gastric mucosa cells than in non-infected counterparts. We did not observed any difference in the efficiency of repair of DNA lesions induced by HCAs in both type of cells. Vitamin C reduced the genotoxic effects of HCAs in H. pylori infected and non-infected gastric mucosa cells. Melatonin more effectively decreased DNA damage caused by HCAs in H. pylori infected gastric mucosa cells as compared with control. Our results suggest that H. pylori infection may influence the susceptibility of gastric mucosa cells to HCAs and dietary antioxidative substances, including vitamin C and melatonin may inhibit the genotoxic effects of HCAs on gastric mucosa cells and may reduce the risk of carcinogenesis caused by food borne mutagens and H. pylori infection.     

Transition metal-carbonyl labeling of biotin and avidin for use in solid-phase carbonyl metallo immunoassay (CMIA)

The preparation of several transition metal-carbonyl tracers of biotin and avidin is described. Multiple labeling of avidin was achieved by acylation of some of its amine-bearing residues with N-succinimidyl 4-pentynoate (dicobalt hexacarbonyl). By varying the initial amount of this complex, protein conjugates with the extent of derivatization of up to 13 were obtained. Biotin was labeled with one (eta5-cyclopentadienyl)manganese tricarbonyl moiety by reaction of biotin hydrazide, whereas multiple labeling was reached by successive conjugation of biotin and N-succinimidyl 4-pentynoate (dicobalt hexacarbonyl) or (eta5-cyclopentadienyl)iron dicarbonyl (eta1-N-maleimidato) to poly-L-lysine or fourth generation Starburst dendrimer. All the conjugates displayed a good to excellent bioaffinity toward their respective counterparts, as measured by competitive enzymatic assays.     

Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes

Several bacterial genera express proteins that contain collagen-like regions, which are associated with variable (V) non-collagenous regions. The streptococcal collagen-like proteins, Scl1 and Scl2, of group A Streptococcus (GAS) are members of this 'prokaryotic collagen' family, and they too contain an amino-terminal non-collagenous V region of unknown function. Here, we use recombinant rScl constructs, derived from several Scl1 and Scl2 variants, and affinity chromatography to identify Scl ligands present in human plasma. First, we show that Scl1, but not Scl2, proteins from different GAS serotypes bind the same ligand identified as apolipoprotein B (ApoB100), which is a major component of the low-density lipoprotein (LDL). Scl1 binding to purified ApoB100 and LDL is specific and concentration-dependent. Furthermore, the non-collagenous V region of the Scl1 protein is responsible for LDL/ApoB100 binding because only those rScls, constructed by domain swapping, which contain the V region from Scl1 proteins, were able to bind to ApoB100 and LDL ligands, and this binding was inhibited by antibodies directed against the Scl1-V region. Electron microscopy images of Scl1-LDL complexes showed that the globular V domain of Scl1 interacted with spherical particles of LDL. Importantly, live M28-type GAS cells absorbed plasma LDL on the cell surface and this binding depended on the surface expression of the Scl1.28, but not Scl2.28, protein. Phylogenetic analysis showed that the non-collagenous globular domains of Scl1 and Scl2 evolved independently to form separate lineages, which differ in amino acid sequence, and these differences may account for the variations in binding patterns of Scl1 and Scl2 proteins. Present studies provide insight into the structure-function relationship of the Scl proteins and also underline the importance of lipoprotein binding by GAS.     

A calcium-binding protein with similarity to serum albumin localized to the ER-Golgi network and cell walls of spinach (Spinacia oleracea)

Using polyclonal antibodies raised against human serum albumin (HSA), a 70-kDa microsomal protein with an isoelectric point of approximately 6.5 was detected in spinach ( Spinacia oleracea L.). The protein was purified by selective ammonium sulfate precipitation and anion exchange HPLC. The protein shared 100% identity with the first 15 amino acids at the NH₂ terminus of HSA, including the X-X-H amino acid region, which was identified in HSA as being responsible for binding of copper, zinc, indole derivatives and calcium. Blue staining of the protein with the cationic carbocyanine dye 'Stains-all' and ⁴⁵Ca overlay following SDS-PAGE also suggest that the 70-kDa plant protein binds calcium. The protein reacted positively with carbohydrate specific thymol stain, and the carbohydrates associated with the protein were identified by gas chromatography-mass spectrometry (GC-MS) as galactose and galacturonic acid. The 70-kDa plant protein was present in the detergent-poor phase following Triton X-114 extraction of the microsomal proteins. Cell fractionation using continuous sucrose gradients showed that the protein is present in membrane fractions with high activity of endoplasmic reticulum (ER) and Golgi marker enzymes. Using nitrocellulose tissue prints probed with anti-HSA antibodies, we demonstrated that the protein is present in the apoplastic space of petioles, suggesting that the protein is secreted to the apoplast of cortex cells in plants. Localization and binding properties suggest that the plant protein identified in the present study may participate in secretion processes, possibly involved with the transport of precursors required for cell-wall synthesis.     

The Influence of Spike Rate and Stimulus Duration on Noradrenergic Neurons

We model spiking neurons in locus coeruleus (LC), a brain nucleus involved in modulating cognitive performance, and compare with recent experimental data. Extracellular recordings from LC of monkeys performing target detection and selective attention tasks show varying responses dependent on stimuli and performance accuracy. From membrane voltage and ion channel equations, we derive a phase oscillator model for LC neurons. Average spiking probabilities of a pool of cells over many trials are then computed via a probability density formulation. These show that: (1) Post-stimulus response is elevated in populations with lower spike rates; (2) Responses decay exponentially due to noise and variable pre-stimulus spike rates; and (3) Shorter stimuli preferentially cause depressed post-activation spiking. These results allow us to propose mechanisms for the different LC responses observed across behavioral and task conditions, and to make explicit the role of baseline firing rates and the duration of task-related inputs in determining LC response.